graph TD
  subgraph Input data
    A[Extant genomes]
    B[Species tree]
    C[Gene phylogenies]
    D[Extant gene orders]
  end
  subgraph AGORA
    E[Ancestral gene lists]
    F{{Reconstruction}}
  end
  subgraph Output
    G[Ancestral Genomes]
  end
  A -.- B & C & D
  C --> E
  B & E & D --> F --> G
